The interlayer coupling in van der Waals (vdW) crystals has substantial effects on the performance of materials. However, an in-depth understanding of the microscopic mechanism on the defect-modulated interlayer coupling is often elusive, owing partly to the challenge of atomic-scale characterization. Here we report the native Se-vacancies in a charge-density-wave metal 2H-NbSe₂, as well as their influence on the local atomic configurations and interlayer coupling. Our low-temperature scanning tunneling microscopy (STM) measurements, complemented by density functional theory calculations, indicate that the Se-vacancies in few-layer NbSe₂ can generate obvious atomic distortions due to the Jahn–Teller effect, thus breaking the rotational symmetry on the nanoscale. Moreover, these vacancies can locally generate an in-gap state in single-layer NbSe₂, and more importantly, lead to a colossal suppression of interlayer coupling in the bilayer system. Our results provide clear structural and electronic fingerprints around the vacancies in vdW crystals, paving the way for developing functional vdW devices.